Other Countries Partnering Award, Canada; Common Genomics Platforms for Oat Breeding
Lead Research Organisation:
Aberystwyth University
Department Name: IBERS
Abstract
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Organisations
- Aberystwyth University (Lead Research Organisation, Project Partner)
- Plant Breeding and Acclimatization Institute (Collaboration)
- Agriculture and Agriculture-Food Canada (Collaboration, Project Partner)
- Dalhousie University (Collaboration)
- IPK Gatersleben (Collaboration)
- University of Life Sciences in Lublin (Collaboration)
- East Malling Research (United Kingdom) (Project Partner)
Publications
Chaffin AS
(2016)
A Consensus Map in Cultivated Hexaploid Oat Reveals Conserved Grass Synteny with Substantial Subgenome Rearrangement.
in The plant genome
Feurtado JA
(2020)
The Hidden Half: Platform Development for Probing Crop Root Systems
Maughan P
(2019)
Genomic insights from the first chromosome-scale assemblies of oat (Avena spp.) diploid species
in BMC Biology
Yan H
(2016)
High-density marker profiling confirms ancestral genomes of Avena species and identifies D-genome chromosomes of hexaploid oat.
in TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik
| Description | Genomic resources developed at Aberystwyth have been used by the Canadian partners to produce an exome capture design which recovers the majority of the protein coding sequences from the hexaploid genome. This represents a roughly 100-fold enrichment of the most significant functional regions, greatly increasing the efficiency of genome sequencing. The Canadian partners have used the captured sequences to look at the evolution of the more diverse wild relatives of oat, and at the variation within elite lines, while the UK partner has looked at diversity and genetic bottlenecks associated with oat domestication and the shift from landraces to modern varieties.Preliminary work carried out during this project has been developed further on two subsequent UK awards. The partners have also worked closely on the development and application of a high-throughput genotyping platform, with creation of a consensus map for the IBERS experimental Nested Association Mapping (NAM) population, which is enabling discovery of candidate genes. Meetings supported by the award led to the formation of a consortium to complete the hexaploid red oat genome and use this reference to anchor genetic diversity identified through high throughput genotyping and exome capture analyses. |
| Exploitation Route | Exome capture design and data will allow identification of key genetic variation underpinning adaptation and beneficial agronomic traits, including disease and biotic stress resistance. Understanding the function of these variants will allow trait dissection and inform more intelligent strategies to develop improved and novel varieties, for example to improve the 'healthy' aspects of oat products by altering beta-glucan and starch properties. |
| Sectors | Agriculture, Food and Drink |
| Description | The workshops and exchanges supported by this award helped establish PanOat, an international consortium with over 50 members which is assembling and annotating more than 30 oat genome reference sequences. Partners include major publically funded research groups and commercial organisations in Europe, North America and Australia. The resources developed will significantly enhance the value of individual national funding and benefit oat breeding programmes globally by improving prediction of crop performance and by accelerating identification and exploitation of critical genetic variation. Oat is a relatively low input and low intervention crop with proven health promoting properties, and there is broad value in increasing its contribution to agricultural output. |
| First Year Of Impact | 2020 |
| Sector | Agriculture, Food and Drink |
| Impact Types | Economic |
| Description | Genotypic characterisation of oat ex situ germplasm collections |
| Amount | £145,000 (GBP) |
| Funding ID | BBS/OS/GC/200011 |
| Organisation | Biotechnology and Biological Sciences Research Council (BBSRC) |
| Sector | Public |
| Country | United Kingdom |
| Start | 11/2017 |
| End | 07/2018 |
| Description | OECD co-operative research programme |
| Amount | $25,000 (CAD) |
| Organisation | Organisation for Economic Co-operation and Development OECD |
| Sector | Public |
| Country | France |
| Start | 04/2019 |
| End | 08/2019 |
| Description | Oat domestication - understanding the origin of a European cereal |
| Amount | £548,306 (GBP) |
| Funding ID | BB/S008195/1 |
| Organisation | Biotechnology and Biological Sciences Research Council (BBSRC) |
| Sector | Public |
| Country | United Kingdom |
| Start | 12/2018 |
| End | 06/2021 |
| Description | TR Newton Fund (to Dr Ziya Dumlupinar) |
| Amount | £2,484 (GBP) |
| Funding ID | 261857630 |
| Organisation | British Council |
| Sector | Charity/Non Profit |
| Country | United Kingdom |
| Start | 07/2017 |
| End | 08/2017 |
| Title | Exome capture design for oats |
| Description | An exome capture array, targetting 70% of the gene complement, was designed by our partners at AAFC Ottawa, using a variety of transcriptome resources aligned to the IBERS Avena atlantica genome contigs. The Ottawa lab has captured genic sequences from a range of Avena species, both diploid and polyploid, and will use the data to clarify relationships between species. Genic sequences have been recovered for 24 IBERS hexaploid accessions, including NAM population parents and key wild or weedy oat relatives. The combined data will be used to refine the capture design, which may then be deployed to look in more detail at patterns of diversity and targets of selection during adaptation and domestication in panels of cultivars, landraces and wild relatives. |
| Type Of Material | Technology assay or reagent |
| Year Produced | 2017 |
| Provided To Others? | No |
| Impact | Funding is being sought for further application of the capture design. |
| Title | Nested Association Mapping (NAM) population for spring oats |
| Description | Fourteen diverse hexaploid cultivars were crossed with the widely used European spring oat cultivar Firth. 650 lines were derived by single seed descent and advanced generations (F8 on) grown for three years at Aberystwyth and one year in Lublin, Poland (collaboration with Dr Edyta Paczos-Grzeda). RNAseq of developing grain was carried out for all parents. Seed and DNA were saved for the F4 generation of all lines, allowing lines heterozygous for alleles of interest to be identified and used to produce HIFs (contrasting alleles in near identical genetic backgrounds). Exome capture with the Ottawa diploid-based design was carried out on all parents, with skim sequencing and FISHIS libraries of the common parent.. |
| Type Of Material | Biological samples |
| Year Produced | 2018 |
| Provided To Others? | Yes |
| Impact | A consensus map is being created. Candidate gene mapping has identified a candidate for the N1 (naked) gene (collaboration with the Tinker lab, Ottawa). |
| Title | Hexaploid oat reference genome |
| Description | A reference genome is being constructed for the hexaploid red oat (A. byzantina) in collaboration with Dr Martin Mascher, IPK, Gatersleben. |
| Type Of Material | Database/Collection of data |
| Year Produced | 2018 |
| Provided To Others? | No |
| Impact | The reference genome is being used to anchor high throughput genetic markers (genotyping-by-sequence) associated with important agronomic traits to sequence scaffolds, which allows the identification of likely candidate genes for further validation. Target genes under analysis (March 2019) include those responsible for grain shattering, naked grain, flowering time, grain beta-glucan content and plant height. |
| Title | NAM maps |
| Description | Genotyping and mapping of the first oat Nested Association Mapping (NAM) population has been carried out. genotyping-by-sequence (GbS) libraries were constructed in Canada (Laval), sequenced at IBERS and genotyping data analysed at IBERS using software (Haplotag) developed by the Tinker lab, Ottawa. |
| Type Of Material | Database/Collection of data |
| Year Produced | 2016 |
| Provided To Others? | Yes |
| Impact | The NAM map adds considerable value to the oat diploid zipper and hexaploid chromosome assemblies (see BBS/E/W/10962A01C, BB/H009582/1). Combining the databases allows rapid identification of candidate genes underlying QTLs mapped by GbS (global database available through T3/Oat). |
| Description | Dalhousie University |
| Organisation | Dalhousie University |
| Department | Department of Biology |
| Country | Canada |
| Sector | Academic/University |
| PI Contribution | Data sharing (Avena genome assemblies) |
| Collaborator Contribution | Advice on methodology, data sharing (Genotype-by-sequence) |
| Impact | None so far |
| Start Year | 2015 |
| Description | IHAR, Polish National Research Institute, Radzików |
| Organisation | Plant Breeding and Acclimatization Institute |
| Country | Poland |
| Sector | Learned Society |
| PI Contribution | Preliminary genotyping and transcriptome sequencing is underway for two accessions of the tetraploid Avena macrostachya. The genome of one accession will be sequenced to allow construction of a high quality assembly, which will be annotated using the pipelines developed in earlier BBSRC funded projects. |
| Collaborator Contribution | The IHAR partners have created the leading international collection of Avena macrostachya resouces. A publication in 2020 provides the first comprehensive description of genetic diversity across the range of A. macrostachya populations, while earlier work included introgression of A. macrostachya germplasm into cultivated hexaploid oats. |
| Impact | Preliminary data only |
| Start Year | 2019 |
| Description | IPK |
| Organisation | IPK Gatersleben |
| Country | Germany |
| Sector | Private |
| PI Contribution | Genetic and physical resources needed to support genomics programme - mapping populations, initial genotyping and selection of key accessions, genomic DNA and specific tissue RNA isolation, resource management, genome annotation |
| Collaborator Contribution | Genome assembly expertise, including modelling of most efficient sequencing strategies, implementation of bioinformatic pipelines, provision of specialised computing facilities and data analysis |
| Impact | Assembly of a reference genome for red oat, Avena byzantina. |
| Start Year | 2017 |
| Description | Morden |
| Organisation | Agriculture and Agri-Food Canada |
| Department | Morden Research and Development Centre |
| Country | Canada |
| Sector | Public |
| PI Contribution | Access to genomic and transcriptomic data |
| Collaborator Contribution | Genetic resources and expertise |
| Impact | OECD fellowship awarded to Canadian RA for 4 month research visit |
| Start Year | 2017 |
| Description | University of Life Sciences, Lublin |
| Organisation | University of Life Sciences in Lublin |
| Country | Poland |
| Sector | Academic/University |
| PI Contribution | Bioinformatics support and access to genomics databases, characterisation of hybrid populations |
| Collaborator Contribution | Population and genetic marker development, field trials and phenotyping of cultivated and hybrid oats. |
| Impact | Identification of candidate genes for key agronomic traits (height, disease resistance). Training and exchange of support staff. Collaboration in BBSRC 'Oat domestication' Avena byzantina and A. sterilis sequencing project. Collaboration with international PanOat consortium for hexaploid oat genome sequencing, assembly and annotation. |
| Start Year | 2016 |
| Description | University of Life Sciences, Lublin |
| Organisation | University of Life Sciences in Lublin |
| Country | Poland |
| Sector | Academic/University |
| PI Contribution | Bioinformatics support and access to genomics databases, characterisation of hybrid populations |
| Collaborator Contribution | Population and genetic marker development, field trials and phenotyping of cultivated and hybrid oats. |
| Impact | Identification of candidate genes for key agronomic traits (height, disease resistance). Training and exchange of support staff. Collaboration in BBSRC 'Oat domestication' Avena byzantina and A. sterilis sequencing project. Collaboration with international PanOat consortium for hexaploid oat genome sequencing, assembly and annotation. |
| Start Year | 2016 |
| Description | Aberystwyth Partnering Workshop 2015 |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Professional Practitioners |
| Results and Impact | A workshop was held to discuss oat genotyping and genomics, and to provide hands-on training in new software. Two senior Canadian researchers (Dr Nick Tinker, AAFC Ottawa and Dr Robert Latta, Dalhousie University) were invited, with their travel and subsistence covered by the Partnering award. Dr Jess Schlueter (University of North Carolina at Charlotte) and Dr Giorgio Tumino (CRA, Fiorenzuola and Wageningen University) also attended, with independent funding and some support from Aberystwyth University. A number of IBERS colleagues also participated. Sessions covered genetic resources and selection of diverse material for future genotyping, phylogenetic analyses and sampling strategies, genome sequencing and genotyping-by-sequence (GbS) analyses. Use of Dr Tinker's new Haplotag software was demonstrated with hands-on analysis of new data from the IBERS' NAM population. The workshop provided valuable training which has been put to good use with further NAM GbS analysis. Progress on the existing Avena Ancestors project, led by Dr Tinker, and on the hexaploid oat genome sequencing project, led by Dr Schlueter, was reviewed and future plans confirmed. Possible extensions of these projects to include further European collaboration were discussed. IBERS colleagues were updated on oat programmes and provided valuable suggestions for analyses, which they have since helped to carry out. |
| Year(s) Of Engagement Activity | 2015 |
| Description | Oat Breeders exchange |
| Form Of Engagement Activity | A formal working group, expert panel or dialogue |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Professional Practitioners |
| Results and Impact | Senior oat breeders from IBERS visited colleagues at major breeding programmes in Canada (Saskatoon, Brandon, Ottawa).Tours of facilities and discussions about best practice and new approaches were very useful, and strengthened existing collaborations. |
| Year(s) Of Engagement Activity | 2017 |
| Description | Oat breeding programme exchange |
| Form Of Engagement Activity | A formal working group, expert panel or dialogue |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Professional Practitioners |
| Results and Impact | Researchers from IBERS and University of Lublin visited oat breeding programmes in Canada to discuss best practice and potential collaborations for application of new genomics and disease resistance resources. A successful application for an OECD visiting fellowship was subsequently made to support a four month visit by a Canadian researcher to the UK group, and a broader international consortium has been formed to develop a platform for identification of relevant candidate genes. |
| Year(s) Of Engagement Activity | 2018 |
| Description | Oat disease resistance workshop |
| Form Of Engagement Activity | A formal working group, expert panel or dialogue |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Professional Practitioners |
| Results and Impact | A meeting was held in Aberystwyth to discuss application of developing genomics resources to discovery and exploitation of genetic resistance to fungal diseases of oat such as rust and mildew. International experts from Australia and Poland attended, and future collaborations were planned. |
| Year(s) Of Engagement Activity | 2018 |
| Description | Oat genomics workshop 2018 |
| Form Of Engagement Activity | A formal working group, expert panel or dialogue |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Professional Practitioners |
| Results and Impact | Colleagues from US, Canadian, Polish, German and Swedish labs contributed to discussions about ongoing genome analyses in wild and cultivated Avena species. Future funding and strengthened collaboration plans were confirmed. A direct result of the meeting was the successful application for BBSRC funding for the 'European cereal - oat domestication' project. |
| Year(s) Of Engagement Activity | 2018 |
| Description | Oat quantitaive genetics workshop |
| Form Of Engagement Activity | A formal working group, expert panel or dialogue |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Professional Practitioners |
| Results and Impact | Colleagues from Canada, Ireland and UK met to discuss genomic selection approaches to improved oat breeding in their respective programmes. |
| Year(s) Of Engagement Activity | 2018 |
| Description | PAG XXV, 2017 |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Professional Practitioners |
| Results and Impact | The International Plant and Animal Genome conference (PAG) is the the Largest Ag-Genomics Meeting in the World. It brings together over 3,000 leading genetic scientists and researchers in plant and animal research, and over 130 exhibits, 150 workshops, 1100 posters and over 1800 abstracts.Two talks and two posters were presented by Tim Langdon; Workshop talks "Oats - Contacting the Uncontacted Genome", "Introgressions in an Oat Nested Association Mapping Population Speaker" Posters "Fine Mapping of the Dw7 Dwarfing Gene in Oat", "Identifying Avena-specific genes" Dr Langdon was also an organiser of the Oats workshop, participated in discussions with NRgene and various public good research labs about hexaploid oat genome sequencing initiatives, and arranged side meetings to prepare an ERA-CAPS funding application, and to establish an informal consortium for assembly and annotation of oat sequencing data. |
| Year(s) Of Engagement Activity | 2017 |
| URL | http://www.intlpag.org/ |
| Description | ScanOat meeting |
| Form Of Engagement Activity | A formal working group, expert panel or dialogue |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Industry/Business |
| Results and Impact | Discussion of IBERS interaction with newly established Swedish ScanOat research centre, specifically genomics research and dihaploid production. ScanOat have expressed support for genomics research at IBERS (BBSRC RM application) and spin-out company Crop Tailor are seeking to collaborate with IBERS, Senova and Saaten Union/Nordsaat on further development of dihaploid production. |
| Year(s) Of Engagement Activity | 2017 |